Question: What Is The Best Program To Determine Structural Variation (Cnv) For Illumina Omniexpress Data?
gravatar for Biomed
8.4 years ago by
Bethesda, MD, USA
Biomed4.5k wrote:

We have been using PennCNV to determine copy number variations from illumina snp chip data in our lab. We have recently started using Illumina Omniexpress chips. I know that we need to create a population B allele frequency file from our samples but I was also wondering if there was a better program for Copy Number Variation analysis using the data from this platform( Illumina OmniExpress) or is there a better option than PennCNV that we should look into?



sv illumina cnv structural • 5.3k views
ADD COMMENTlink modified 7.2 years ago by liutao19860 • written 8.4 years ago by Biomed4.5k

BirdSuite from Broad Institute has beta support for Illumina 610, but no word on Omniexpress. Also for 3rd party, I think GoldenHelix supports Illumina.

ADD REPLYlink written 8.3 years ago by jvijai1.1k
gravatar for Eminencegrise
8.4 years ago by
Eminencegrise210 wrote:

I worked with KaryoStudio and it was rather good. It is proposed by Illumina, have You tried that?

ADD COMMENTlink modified 8.4 years ago by Eric Normandeau10k • written 8.4 years ago by Eminencegrise210

Thanks for the suggestion. We use Genome Studio but I don't think it comes with KaryoStudio. Do you need to buy it, if so, do you know how much is it? Have you used any opensource alternatives and especially benchmarked them with KaryoStudio? Thanks

ADD REPLYlink written 8.4 years ago by Biomed4.5k

I had it in as a package with order ( I think there was no serial key needed as it is with Genome Studio), I will look for alternatives as I havent used any. The only problem was that older version (comes on a CD/DVD) of KaryoStudio had no plugin for UPD detection (corrected with update). KS was definately way better solution compared to Genotyping Console (Affymetrix).

ADD REPLYlink written 8.4 years ago by Eminencegrise210
gravatar for Cling
8.3 years ago by
Cling10 wrote:

Hi there... Do you know where to download penncnv .hmm, .pfb, .gcmodel for Illumina Human OmniExpress v.1 chip? Thanks!

ADD COMMENTlink written 8.3 years ago by Cling10

Hi, It is best if you ask new questions as well, "new questions" but here is your answer. You should use your own data to create your own pfb file using the script that comes with penncnv package. You don't need to use a different hmm file, the old "hmmall" file works fine with omniexpress too.

ADD REPLYlink written 8.3 years ago by Biomed4.5k
gravatar for August
8.1 years ago by
August10 wrote:

You should use two separate "wide" methods to identify CNVRs. The two with the highest reviews and that are most commonly used in high impact papers are PennCNV and QuantiSNP. Afterward, consolidate the CNV calls into CNVRs. For each CNVR use a "deep" method to genotype your samples. I recommend CNVtools. You could also use CNVhap to do both simultaneously, but you would have to break the genome down into several hundred peices. Good luck!

ADD COMMENTlink written 8.1 years ago by August10
gravatar for liutao1986
6.9 years ago by
liutao19860 wrote:

Where can i download QuantSNP?? When downloaded from this website ,it was require an username and password... thanks

ADD COMMENTlink written 6.9 years ago by liutao19860
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